I think we are on the same page, yes. Get everything set up first. Run the same length of lines which is the critical part. The doesn't won't know or care about any valves. I'm assuming you will run the DOS AWS task but it assumes you run the get started setup which includes calibration. Thus setting up everything first, verifying the line lengths, run initial setup, then task.
Note that I've not done what you are suggesting but just walking through how I would do it or think it should work. So I do believe we are on the same page. Once you finish the task you could setup a test and do a gallon change on each to see if it is close. That would be easy to correct if so.
Hope your day is going well.
Edit: suncrestreef (user name I believe) has a few threads on auto water changes. Not doing this but at least covers the setup or how he does it. He is a good person and Neptune savvy. If it helps any.